Biological Molecules 2 Flashcards
What are proteins made of?
Proteins are biopolymers composed of α-amino acids
What determines the physical and chemical properties of a protein?
The constituent amino acids
What are the main functions of proteins?
DNA replication, RNA transcription, protein translation
Catalysis of biomolecule transformation
Cellular signaling with polysaccharides
Regulation of lipid bilayers
Transport of molecules across membranes
What is the general structure of an amino acid?
An amino group (-NH₂) bonded to an α-carbon, a carboxyl group (-COOH), a hydrogen, and a side chain (R group).
What is the significance of amino acid stereochemistry?
All natural amino acids (except glycine) are chiral and have the L-configuration
Which amino acid has an R-configuration but is still an L-amino acid?
Cysteine (R=CH₂SH)
How are amino acids classified based on R group polarity?
Hydrophobic (nonpolar)
Polar, uncharged
Charged (acidic or basic)
How do hydrophobic amino acids contribute to protein structure?
They cluster internally, stabilizing the 3D structure via the hydrophobic effect.
What is the isoelectric point (pI)?
The pH at which an amino acid exists as a zwitterion (neutral net charge).
What is a peptide bond?
A covalent bond between the α-carboxyl group of one amino acid and the α-amino group of another, formed via condensation.
How are peptide bonds read?
From the N-terminal (left) to the C-terminal (right)
What are the four levels of protein structure?
Primary – Amino acid sequence
Secondary – α-helices & β-sheets
Tertiary – 3D folding of a polypeptide
Quaternary – Association of multiple polypeptides
What stabilises secondary structures?
Hydrogen bonds between backbone atoms.
What is the difference between α-helix and β-sheet?
α-helix: Coiled, stabilized by H-bonds (n+4 rule).
β-sheet: Extended zig-zag, held by H-bonds between adjacent strands
What is the function of disulfide bonds in proteins?
Covalent cross-links between cysteine residues, stabilizing the 3D structure
What are the essential amino acids?
Arginine (Arg), Valine (Val), Histidine (His), Methionine (Met), Leucine (Leu), Threonine (Thr), Lysine (Lys), Phenylalanine (Phe), Tryptophan (Trp), and Isoleucine (Ile) – these must be obtained from the diet
What are rare and unusual amino acids?
Hydroxylated versions of standard amino acids, often found in collagen and other specialized proteins.
What are amphoteric properties of amino acids?
Amino acids can act as both acids and bases, existing in different forms depending on pH:
Low pH: Protonated form (+ charge)
Neutral pH: Zwitterion (no net charge)
High pH: Deprotonated form (- charge)
What is the titration curve of glycine?
Glycine has two distinct pKa values:
pH 2.3: Half the cationic form is converted to the zwitterionic form.
pH 9.6: Half the zwitterionic form is converted to the basic form.
Isoelectric point (pI): pH 5.97, where glycine exists mainly as a neutral zwitterion.
What are the pKa values of charged amino acids?
Acidic: Aspartic acid (pKa ≈ 3.7), Glutamic acid (pKa ≈ 4.2)
Basic: Histidine (pKa ≈ 6.0), Lysine (pKa ≈ 10.7), Arginine (pKa ≈ 12.1)
What is transamination in amino acid synthesis?
A reaction in which an amino group is transferred to an α-keto acid, forming a new amino acid. Most L-amino acids except lysine, threonine, proline, and hydroxyproline undergo transamination
What is the Strecker synthesis of amino acids?
A synthetic method using aldehydes, ammonium chloride (NH₄Cl), and cyanide (HCN) to form α-amino acids. It produces a racemic mixture of D- and L- amino acids
What is a peptide bond’s resonance structure?
Due to resonance, the peptide bond has partial double bond character, making it rigid and planar. This restricts rotation around the C-N bond, affecting protein folding.
What is the difference between cis and trans peptide bonds?
Trans: R-groups are on opposite sides of the peptide bond (favored in >99% of cases).
Cis: R-groups are on the same side, leading to steric hindrance (only Proline commonly forms cis bonds)
What are the different types of secondary structures?
α-helix: Right-handed coil stabilized by H-bonds (common in L-amino acids).
β-sheet: Formed by adjacent β-strands, either parallel (H-bonds not in-line) or antiparallel (H-bonds in-line).
Loops and Turns: Short segments that reverse polypeptide direction, often containing proline (rigid) or glycine (flexible).
How do amino acids influence secondary structure formation?
Favors α-helix: Alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, lysine.
Favors β-sheet: Valine, isoleucine, phenylalanine, tyrosine, tryptophan, threonine.
Favors turns: Glycine, proline, serine, aspartic acid, asparagine.
What is the hydrophobic effect in protein folding?
Hydrophobic amino acids cluster in the protein’s interior, creating a compact hydrophobic core that stabilises tertiary structure.
What types of interactions stabilise tertiary protein structure?
Hydrogen bonds (between polar side chains)
Ionic bonds (between charged residues)
Van der Waals forces (weak interactions between all atoms)
Disulfide bonds (covalent bonds between cysteine residues)
What is quaternary protein structure?
The 3D arrangement of multiple polypeptide subunits into a functional complex (e.g., hemoglobin is a heterotetramer).
How are peptide sequences named?
Peptides are read from N-terminal to C-terminal.
All residues except the last one use the “-yl” suffix (e.g., Arginyl-Prolyl-Glycyl).
Example: Bradykinin → Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg (RPPGFSPFR)
What is the role of disulfide bonds in protein structure?
Disulfide bonds form between two cysteine residues, strengthening tertiary and quaternary structures. They are reversible upon reduction
What is the difference between oligomers and multimers in proteins?
Oligomers: Small protein complexes (e.g., dimers, trimers, tetramers).
Multimers: Larger protein assemblies.
Homo-oligomers: Identical subunits.
Hetero-oligomers: Different subunits (e.g., hemoglobin is a heterotetramer)
How are amino acids synthesised in biological systems?
Hydrolysis of proteins
Reductive amination (biomimetic synthesis)
Transamination (using enzymes)
Amination of α-halo acids
Strecker synthesis (chemical synthesis)
What are the characteristics of the peptide bond?
Peptide bonds are rigid and planar: due to resonance, both the C-O and C-N
bonds have partial double bond nature (electrons delocalised):
Characteristics of peptide bonds: big role in the 3-D structure of peptides and
proteins (“protein folding”)
Restrict rotation around the C(carbonyl)-N bond: it cannot rotate
freely. Rotation is instead permitted around the N-C α and C
(carbonyl)-C α bonds
